rank.enrichment: Rank enrichment

In cbg-ethz/epiNEM: epiNEM

Rank enrichment

Description

Infers a signalling pathway from peerturbation experiments.

Usage

rank.enrichment(
  data,
  list,
  list2 = NULL,
  n = 1000,
  main = NULL,
  col1 = "RdBu",
  col2 = rgb(1, 0, 0, 0.75),
  col3 = rgb(0, 0, 1, 0.75),
  blim = NULL,
  p = NULL,
  lwd = 3,
  test = wilcox.test,
  vis = "matrix",
  verbose = FALSE,
  ...
)

Arguments

data	m times l matrix with m observed genes and l variables with numeric values to rank the genes
list	list of of vectors of genes
list2	optional list with same length as list
n	length of the gradient (maximum: m)
main	character string for main header; if NULL uses the column names of data by default
col1	color of the gradient
col2	color of the first list
col3	color of the second list2
blim	numeric vector of length two with the lower and upper bounds for the gradient
p	numeric adjustment (length four) of the left side of the gradient (low means more to the left, high more to the right) the right side of the enrichment lines and the top positions of the additional matrices in case of vis='matrices'
lwd	line width of the enrichment lines
test	test function for the enrichment p-value; must have input argument and output values same as perm.rank.test; e.g., wilcox.test or ks.test (here 'less' and 'greater' are switched!)
vis	method for visualisation: 'matrix' uses one matrix heatmap for; 'matrices' uses several matrices (experimental), 'colside' uses the colSideColors argument for the ticks of genes in list/list2 (can use a lot of memory; experimental)
verbose	if TRUE gives prints additional output
...	additional arguments for epiNEM::HeatmapOP

Value

transitively closed matrix or graphNEL

Author(s)

Martin Pirkl

Examples

data <- matrix(rnorm(100*2),100,2)
rownames(data) <- 1:100
colnames(data) <- LETTERS[1:2]
list <- list(first = as.character(sample(1:100, 10)), second = as.character(sample(1:100, 20)))
rank.enrichment(data,list)

cbg-ethz/epiNEM documentation built on Nov. 6, 2024, 4:21 a.m.